H+-gated ion channel

ABSTRACT

The invention relates to an isolated or recombinant Na + /H +  exchanger comprising an isolated or recombinant Na + /H +  exchanger, particularly to the PBO-4 Na + /H +  exchanger. Also disclosed is an isolated or recombinant protein component of an H + -gated channel which can be affected by extracellular Ca 2+  concentration. In particular, the invention relates to PBO-5 and/or PBO-8 and/or a H + -gated channel composed of PBO-5 and PBO-8. The invention relates to compounds isolated from a vertebrate organism, wherein said compounds comprise at least a part of a H + -gated channel or Na + /H +  exchanger. The invention also relates to a method for identifying a component of a H + -gated channel in a vertebrate organism.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of application Ser. No. 12/905,647 filed on Oct. 15, 2010 now U.S. Pat. No. 8,012,702, which is a continuation of application Ser. No. 12/189,014 filed on Aug. 8, 2008 (now U.S. Pat. No. 7,820,791), which is a continuation of application Ser. No. 11/587,018 (now abandoned), which is a National Phase Application of International Application No. PCT/US2005/013415, filed Apr. 20, 2005, which claims priority to U.S. Provisional Application No. 60/563,939, filed Apr. 20, 2004, the entirety of which is incorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Grant MH60997-02 awarded by the National Institute of Health. The government has certain rights in the invention.

TECHNICAL FIELD

This invention relates to biotechnology, more particularly to one or more members of the “cys-loop” ligand-gated ion channel superfamily, which are activated by a proton and/or H⁺/Na⁺ exchange proteins, and methods of using the same.

BACKGROUND

Motor behaviors such as locomotion rely on precise signaling from the nervous system to coordinate various muscle activities. The neuromuscular junction has been extensively studied and a considerable amount of information exists on how information is communicated across the synapse between a motor neuron and a muscle cell. At the cellular level, depolarization of the motor neuron produces an action potential that is propagated to the presynaptic terminal Depolarization causes the opening of voltage-gated calcium channels at the presynaptic terminal, resulting in an increase in intracellular calcium. In response to local increases in calcium, neurotransmitter filled vesicles fuse with the presynaptic plasma membrane, releasing their contents into the synaptic cleft. Postsynaptic ligand-gated ion channels on the muscle bind the neurotransmitter, resulting in the opening of an integral ion channel. Depending on an ion channel's permeability, the muscle is either hyperpolarized or depolarized.

Chemical synaptic transmission mediates fast and slow communication between cells, but it is not the only means of communication within the nervous system. Signals may also be conveyed nonsynaptically. In this case, a neurotransmitter or hormone is released at one site and slowly diffuses to distant target sites that are not in contact with the original site of release. This type of signaling is more suited to global, modulatory activities rather than functions requiring a rapid response. The interplay of synaptic and non-synaptic communication ultimately determines how a nervous system mediates particular behaviors.

In C. elegans, synaptic transmission has been extensively studied at the genetic, cellular and molecular levels. Most behaviors in the worm follow a simple paradigm in which information is directed from the sensory neurons to motor neurons to muscle, via synaptic contacts. However, the defecation cycle in C. elegans is a unique behavior in that it appears to be mediated by both synaptic, as well as nonsynaptic transmission (McIntire et al., 1993b; Thomas, 1990). Defecation in C. elegans is a stereotyped behavior that occurs every 50 seconds for the life of the animal, and is characterized by the coordinated activation of three independent muscle contractions (Croll, 1975; Thomas, 1990). The cycle is initiated with a posterior body contraction, followed by an anterior body contraction and finalized by an enteric muscle contraction, which expels intestinal contents. A simplified genetic pathway to explain the defecation behavior was proposed by Jim Thomas (Thomas, 1990) (see, FIG. 1B). In this model, a clock mechanism keeps time independently of the motor program. At the appropriate interval, the clock first signals the posterior body contraction and then signals the common anterior body and enteric muscle contraction mechanism, which ultimately leads to activation of the individual muscle contractions (Liu and Thomas, 1994; Thomas, 1990) (FIG. 1B).

To determine the cellular basis of the defecation motor program, extensive cellular laser ablations have been performed. Based on these studies the motor neurons AVL and DVB were demonstrated to mediate the anterior body and enteric muscle contraction, but not posterior body contraction (McIntire et al., 1993b). The anterior body contraction is mediated by the motor neuron AVL, but the neurotransmitter that mediates this contraction is unknown (see, FIG. 1A). While AVL alone is required for anterior body contraction, both the AVL and DVB motor neurons serve a redundant function in activating the enteric muscles (see, FIG. 1A). Activation of the enteric muscles is GABA-dependent and is mediated by the EXP-I receptor (Beg and Jorgensen, 2003; McIntire et al., 1993a; McIntire et al, 1993b).

Interestingly, no known neurons are required to maintain the clock or initiate the posterior body contraction, suggesting that cycle timing and posterior body contraction are mediated by a non-neuronal mechanism (Liu and Thomas, 1994; McIntire et al., 1993b; Thomas, 1990) (see, FIG. 1A). Furthermore, mutations that disrupt classical neurotransmission and secretion do not affect the posterior body contraction. Taken together, these data suggest that posterior body contraction occurs through a non-neuronal mechanism that does not rely on classical or peptidergic neurotransmission.

Many genes have been identified that affect only specific aspects of the defecation motor program. It has been demonstrated that timekeeping of the cycle is controlled by an endogenous clock that resides in the intestine (Dal Santo et al., 1999). The cycle time is set by the activity of the itr-1 gene, which encodes an inositol triphosphate (IP3) receptor which mediates release of calcium from the smooth endoplasmic reticulum into the intestine every 50 seconds (Dal Santo et al., 1999). Mutations in the itr-1 gene slow down or eliminate the cycle, while overexpression accelerates the cycle. In the intestine, calcium levels oscillate with the same period as the defecation cycle (50 seconds) and peak calcium levels immediately precede the posterior body contraction (Dal Santo et al., 1999). Therefore, the frequency of intracellular calcium release in the intestine, determines the frequency of the defecation cycle.

It has been demonstrated that there is a one-to-one relationship between the calcium spike in the intestine and the execution of the posterior body contraction (Dal Santo et al., 1999). Normally, motor behaviors such as muscle contraction are mediated by the nervous system. Since neuronal input is not required to initiate the posterior body contraction, these muscles could be directly activated by a Ca²⁺ regulated signal from the intestine.

BRIEF SUMMARY

In accordance with the purpose of this invention, as embodied and broadly described herein, this invention relates to an isolated or recombinant Na⁺/H⁺ exchanger comprising an isolated or recombinant Na⁺/H⁺ exchanger. The invention further relates to the PBO-4 Na⁺/H⁺ exchanger and Na⁺/H⁺ exchangers having at least 80%, 81%,82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and/or 99% identity to PBO-4 (SEQ ID NO:8). Optionally, the isolated or recombinant Na⁺/H⁺ exchanger functions in the intestine.

The invention also relates to isolated or recombinant protein component of an H⁺-gated channel. The invention further relates to a H⁺-gated channel that is effected by extracellular Ca²⁺ concentration. In particular, the invention relates to PBO-5 (SEQ ID NOs: 1 and 2) and/or PBO-8 (SEQ ID NOs: 3-5) and/or a H⁺-gated channel composed of PBO-5 and PBO-8. In addition the invention relates to isolated and/or recombinant proteins having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and/or 99% identity to PBO-5 and/or PBO-8. Further, the invention relates to a H⁺-gated channel that is pH sensitive. The invention further relates to a H⁺-gated cation channel.

The invention relates to compounds isolated from a vertebrate organism, wherein said compounds comprise at least a part of a H⁺-gated channel or Na⁺/H⁺ exchanger. The invention further relates to a Na⁺/H⁺ exchanger identified in a vertebrate organism.

The invention also relates to a method for identifying a component of a H⁺-gated channel in a vertebrate organism. For example, by screening a vertebrate organism for the presence of a component of a H⁺-gated channel; identifying the component of the H⁺-gated channel; and confirming that the component of the H⁺-gated channel is a component of said H⁺-gated channel. Optionally, the method further comprises isolating the component of said H⁺-gated channel.

The invention also relates to screening a component of a H⁺-gated channel for activation or inhibition by a candidate drug. The invention also relates to screening the component of a H⁺-gated channel for binding to HEPES and/or identifying mutations which prevent binding to HEPES.

The invention further relates to a protein produced by a process of screening a vertebrate organism for the presence of a component of a H⁺-gated channel; identifying said component of said H⁺-gated channel; and confirming that said component of said H-gated channel is a component of said H⁺-gated channel.

The invention further relates to compounds according to the invention identified in a mammal.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several embodiments of the disclosed method and compositions and together with the description, serve to explain the principles of the disclosed method and compositions.

FIG. 1 illustrates the defecation cycle behavior and genetics of the defecation cycle in C. elegans. FIG. 1A is a schematic drawing of the defecation cycle. Every 50 seconds a cycle is initiated by the posterior body contraction (pBoc), followed by an anterior body contraction (aBoc), and completed by an enteric muscle contraction, (Emc), which mediates expulsion of intestinal contents. Listed to the right are the motor neurons and neurotransmitters involved in each muscle contraction. FIG. 1B illustrates the genes involved and their affects on the cycle. A 50 second clock independently keeps time of the cycle. Each step of the defecation cycle can be specifically affected by mutation, demonstrating that cycle timing and muscle activation do not rely on one another. Muscle activation of each step occurs independently of the others. However, the anterior body contraction and the enteric muscle contraction share a common mechanism upstream of muscle activation.

FIG. 2 illustrates the structure and molecular cloning of pbo-5. The genomic location of pbo-5 is the last predicted gene on chromosome V, approximately 1.2 kb from the telomere. The middle of FIG. 2 illustrates the exon-intron structure of the pbo-5 gene. Positions of mutations in pbo-5 alleles are shown below the predicted protein structure. Triangles represent the peptide signal, the dotted line is the disulfide-bond, the transmembrane domains are labeled 1-4.

FIG. 3 shows the sequence alignment of PBO-5 and cholinergic subunits. The amino acid sequence for C. elegans PBO-5, PBO-8 (F11C7.1; SEQ ID NO:5), UNC-29, UNC-38, and human alpha 7 nicotinic acetylcholine receptors subunits. Sequences were aligned using clustal X and identities are shaded and boxed. The black and hollow filled triangles denote the signal peptide sequence for PBO-5 and PBO-8, respectively. The dotted line shows the invariant disulfide bond present in all ligand-gated ion channels. Black bars denote the four transmembrane domains.

FIG. 4 shows the pbo-8 genomic structure and a phylogenetic tree. FIG. 4(A) shows the exon-intron structure of pbo-8. The pbo-8 locus consists of 13 exons that span 4.1 kb of the genome. FIG. 4(B) illustrate that PBO-5 and PBO-8 represent novel ligand-gated ion channel subunits. The PBO-5 and PBO-8 subunits cannot be categorized into one of the four ligand-gated ion channel families based on sequence analysis. Alignments were performed using clustal X and the bootstrap method with ‘neighbor-joining’ search was used to create the tree. Bootstrap values of 1,000 replicates are indicated on the tree.

FIG. 5 shows the expression pattern of pbo-5. FIGS. 5A and 5B are confocal images of animals expressing an integrated pbo-5:: gfp fusion gene. The animals are oriented with anterior to the left, and posterior to the right. GFP expression is observed in the most posterior muscle cells (FIG. 5A) and in the neurons RIFL, RIFR, and RIS (FIG. 5B). FIG. 5C is a schematic drawing to illustrate pbo-5 expression within the context of the entire animal.

FIG. 6 illustrates the structure and molecular cloning of pbo-8. The top of FIG. 6A represents the exon-intron structure of pbo-8; below, the predicted protein structure. The triangle represents the predicted signal peptide cleavage site, the dotted line represents the disulfide-bond, and the numbers 1-4 represent the four transmembrane domains. FIG. 6B shows the expression pattern of PBO-8. The left panel is a confocal image of an animal expressing a transcriptional pbo-5::gfp fusion gene. The right panel is a fluorescent image of an animal expressing a transcriptional pbo-8::gfp fusion gene fusion. PBO-8 expression is observed in the most posterior muscle cells, and has overlapping expression with PBO-5, suggesting PBO-8 may oligomerize with PBO-5 to form a functional receptor.

FIG. 7 shows a pH dose-response curve for PBO-5/PBO-8, which form a heteromultimeric H⁺-gated ion channel. PBO-5/PBO-8 expressing oocytes were voltage-clamped at −60 mV and a series of test pH applications (7.2-5.0) were bath applied for 5 seconds. Each point represents the mean current value normalized to the maximum and minimum values. A pH₅₀=6.83±0.01 and Hill coefficient of 9+0.66 were determined for PBO-5/PBO-8 receptors (n=18). Error bars represent s.e.m. Inset, representative traces of PBO-5/PBO-8 dose-response experiments.

FIG. 8 shows PBO-5/PBO-8 ion selectivity. FIG. 8A shows the current-voltage (I-V) relationship of PBO-5/PBO-8 ion channels. The reversal potential determined under control conditions was 10.18±0.80 mV (n=13). Inset, representative traces of an experiment. Note, the strong inward rectification of PBO-5/PBO-8 receptors. FIG. 8B shows Na⁺ permeability. Na ions were replaced with the cation NMDG, in Na⁺ free Ringer's. There is a negative shift in reversal potential (E_(rev)=−82.90±8.13 mV (n=6)) and the inward current in nearly abolished which suggests that Na is the primary charge carrier through the PBO-5/PBO-8 channel. FIG. 8C shows Cl⁻ permeability. Chloride ions were replaced with the anion gluconate, in Cl⁻ free Ringer's. The negligible shift in reversal potential demonstrates that chloride ions do not underlie the ionic conductance through PBO-5/PBO-8 channels (ΔE_(rev)=0.25 mV, P>0.05, two-way ANOVA, (n=8).

FIG. 8D shows K⁺ permeability. Replacement of K⁺ for Na⁺ in the extracellular solution demonstrates PBO-5/PBO-8 ion channels discriminate poorly between monovalent cations. Note the inward current is still present and there was not significant shift in reversal potential compared to control (P>0.05; two-way ANOVA, (n=4), demonstrating PBO-5/PBO-8 is a nonselective cation channel.

FIG. 9 shows calcium permeability. FIG. 9A shows the current-voltage (I-V) analysis of PBO-5/PBO-8 receptors under different Ca²⁺ concentrations. Reversal potentials were measured under 1 mM Ca²⁺ control and 3 mM and 10 mM test Ca²⁻ conditions. Increasing extracellular Ca²⁺ caused a positive shift in reversal potentials suggesting Ca²⁺ is permeable to PBO-5/PBO-8 channels. Note the decreased inward current as extracellular Ca increased. FIG. 9B shows Ca²⁺ permeability in Na⁺ free Ringers. To better resolve Ca²⁺ permeability, the I-V relationships where Ca²⁺ was the only relevant extracellular ion were determined. These data demonstrate PBO-5/PBO-8 ion channels are Ca²⁺ permeable.

FIG. 10 shows that Ca²⁺ and H⁺ compete at the PBO-5/PBO-8 activation site. FIG. 10A shows the results of normalized current amplitude versus test pH at four different extracellular Ca²⁺ concentrations. Increasing Ca²⁺ decreases the pH necessary for half-maximal activation. Currents were normalized to the maximal value at pH 6.0 for each [Ca²⁺]_(o) condition. FIG. 10B shows that a normalized current amplitude of test pH evoked responses at three Ca²⁺ concentrations. Ca²⁺ shifts activation but increasing extracellular does not affect maximal activation. Current were normalized to the value at 1 mM Ca²⁺ for each pH tested.

FIG. 11 illustrates an exemplary embodiment for posterior body contraction in C. elegans. Every 50 seconds, a calcium spike occurs in the intestine the correlates with the initiation of the posterior body contraction. First, IP₃ receptors localized to the smooth endoplasmic reticulum in the intestine are activated every 50 seconds. Activation results in the intracellular rise of Ca²⁺ in the intestine. Second, Ca²⁺ binds to the C-terminal calmodulin-binding domain of PBO-4, thereby activating H⁺ transport activity. Third, PBO-4 transports H⁺ ions out of the intestine acidifying the pseudocoelomic space. Fourth, H⁺ ions bind and activate the PBO-5/PBO-8 receptors expressed in posterior body wall muscle, thereby allowing Na⁺ influx into the cell causing a depolarization and subsequent muscle contraction.

FIG. 12 illustrates the genetic mapping and molecular cloning of pbo-4. FIG. 12(A) illustrates the pbo-4 locus, which maps between daf-12 and egl-15 on the X chromosome. This region contains the cosmids T21B6 and K09C8. Rescue of the posterior body contraction defect by cosmid or subclone is indicated. Below this is an exon-intron structure of pbo-4. Mutations are indicated, black bars denote the extent of deletion alleles within the locus. FIG. 12(B) illustrates the predicted PBO-4 protein domains. The predicted protein consists of a signal peptide, 12 transmembrane domain, a re-entrant loop between transmembrane domains 9 and 10 and an intracellular carboxy-terminal tail that contains a predicted calmodulin binding site.

FIG. 13 shows a sequence alignment of PBO-4 to human Na⁺/H⁺ exchangers. Deduced polypeptide sequence of PBO-4 aligned with human NHE1(P19634), NHE2(Q9UBY0) and NHE3(P48764) are shown. Sequences were aligned with ClustalX tities are shaded and the arrowhead indicates the predicted signal peptide cleavage site. The last translated amino acid of each pbo-4 mutant allele is denoted by a star. The black bars indicate predicted transmembrane domains, and the dotted line denotes the re-entrant loop as determined for NHE1. The boxed sequence indicates the predicted calmodulin binding domain. The positions of the GFP insertions are indicated by triangles.

DETAILED DESCRIPTION

As used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. For example, reference to “a host cell” includes a plurality of such host cells.

As used herein a “Substantially Identical” polypeptide sequence means an amino acid sequence which differs from a reference sequence only by conservative amino acid substitutions, for example, substitution of one amino acid for another of the same class (for example, valine for glycine, arginine for lysine, etc.) or by one or more non-conservative substitutions, deletions, or insertions located at positions of the amino acid sequence which do not destroy the function of the polypeptide (assayed, for example, as described herein). Preferably, such a sequence is at least 80-100%, more preferably at least 85%, and most preferably at least 90% substantially identical at the amino acid level to the sequence used for comparison.

To identify the nature of the signal, source, and target, screens for mutations affecting the defecation cycle and in particular, mutations specifically affecting the posterior body contraction have been performed. From these screens, only three genes, pbo-1, pbo-4 and pbo-5 result in a specific loss of posterior body contraction, without affecting any other aspect of the defecation motor program. The pbo-1 gene has not been cloned. The pbo-4 gene encodes a putative Na⁺/H⁺ exchanger and is required for activation of the posterior body contraction (P. Dal Santo, personal communication; see Discussion). Its expression in the posterior intestine suggests that pbo-4 functions as a mediator between the calcium signal of the clock in the intestine and the muscle receptor that stimulates the posterior body contraction.

Na⁺/H⁺ exchangers have been implicated in numerous physiological processes such as intracellular pH homeostastis, cell volume regulation, and reabsorption of NaCl across epithelial cells. However, the proton can be involved in more complex cellular processes other than intracellular pH regulation. Deletion of genes involved in H⁺ secretion and reception results in a broad range of cellular and behavioral phenotypes. Significantly, deletion of the murine NHE1 gene reveals it is required for functions as diverse as pH homeostasis to cell morphology and adhesion. Consistent with a broader role for protons as intercellular messengers, a large family of proton-gated channels, termed the acid-sensing ion channels (ASICs), have been identified. Knockouts of specific ASIC family members have demonstrated that proper H⁺ signaling is required not only for sensory modalities such as nociception and mechanoreception, but also for synaptic plasticity and learning and memory in the brain. While specific H⁺-gated receptors such as ASIC1 are expressed in hippocampal neurons, the source of protons required to activate these receptors remains a mystery. Hence, the present invention is useful in the field of medicine and provides valuable research tools for the identification of medical and veterinary compounds.

The gene pbo-5 gene encodes a novel H⁺-gated ion channel subunit. When expressed in Xenopus oocytes, PBO-5 co-assembles with the PBO-8 subunit to form a functional H⁺-gated nonselective cation channel. PBO-5 and PBO-8 are expressed in the posterior body wall muscles, suggesting these two subunits are localized to the appropriate tissues to mediate posterior body contraction. The channel encoded by PBO-5/8 is an inwardly-rectifying non selective cation channel. The molecular identification of the PBO-5 and PBO-8 receptor subunits defines a unique class of the cys-loop ligand-gated ion channel superfamily, and demonstrates a non-neuronal signaling mechanism. Furthermore, the functional characterization of H⁺ sensitivity demonstrates that the PBO-5/8 signaling pathway defines a novel mechanism of cellular communication that relies on H⁺ as a physiological transmitter.

Methods

Molecular Characterization of pbo-5 and pbo-8

The sequence of the pbo-5 transcript was determined by reverse transcription of wild-type RNA followed by PCR amplification (RT-PCR) and direct sequencing. The 5′ trans-spliced sequence was obtained by PCR amplification using an SL1 primer and a nested, gene specific primer in the second exon. The 3′ sequence was obtained by PCR amplification with nested primers in the third predicted exons and with an oligo-dT primer. PCR products were cloned into the pCR2.1 TA cloning vector (Invitrogen) and a full length clone pPD68 was generated.

PBO-8 cDNAs were isolated by RT-PCR. We determined the 5′ end of the gene by circular RACE (Maruyama et al., 1995). The 3′ end of the gene was based on computer prediction and sequence similarity to PBO-5. To isolate full-length cDNAs, oligonucleotide primers were designed to the 5′ and 3′ untranslated regions of pbo-8. PCR products were cloned into pCR2.1, and subsequent products were sequenced to generate a full-length error free PBO-8 cDNA.

Electrophysiology of PBO-5 and PBO-8

To generate plasmid constructs for Xenopus oocyte expression, the foil length error-free cDNA was subcloned into the pSGEM expression vector (courtesy M. Hollmann). The pbo-5 expression vector was constructed by cutting the pPD70 plasmid with restriction enzymes SacII and Eagl, then using T4 DNA polymerase to blunt the ends. Cut products were gel purified (Qiagen) and re-ligated using T4 DNA ligase (Promega) to create the plasmid pAB20. The PBO-8 expression construct was made by cutting a previously sequenced error-free cDNA (M. Peter, unpublished). The cDNA was first cloned into the pSGEM expression vector. Next, the restriction enzymes SacII and BsaBI were used to cut the plasmid, and the ends were blunted with T4 DNA polymerase. Cut products were gel purified and re-ligated to produce pAB21.

Capped RNA was prepared using the T7 mMessage mMachine kit (Ambion). Xenopus oocytes were collected and coinjected with 25 ng each of PBO-5 and PBO-8 cRNA and two-electrode voltage clamp recordings were performed 3-5 days post-injection. The standard bath solution for dose-response and control I-V experiments was Ringer's (in mM): 115 NaCl, 1.8 BaCl2, 10 Bis-Tris Propane (pH 7.4 Acetic acid). For dose-response experiments, each oocyte was subjected to a 5 second application of test pH (7.0 - 5.0) with 2 minutes of pH 7.4 wash between test applications.

Ion selectivity experiments: All points are responses to test pulse applications of pH 6.8 for 5 seconds. The reversal potential of PBO-5/PBO-8 expressing oocytes were first determined in standard Ringer's (in mM): 115 NaCl, 1.0 CaCl2, 10 Bis-Tris Propane (pH 7.4, acetic acid). For chloride permeability a simplified solution was used, chloride-free (in mM): 115 Na⁺ gluconate, 1.0 CaCl₂, 10 Bis-Tris Propane (pH 7.4 acetic acid). For Na⁺ permeability a simplified solution was used, Na⁺ free (in mM): 115 mM N-methyl D-glucamine (NMDG), 1.8 CaCl₂, 10 Bis-Tris Propane (pH 7.4 acetic acid)). All solutions were brought to pH by addition of NaOH or acetic acid. To determine K⁺ permeability, I-V experiments were performed in K⁺ Ringer's (in mM): 115 K⁺-gluconate, 1.0 CaCl₂, 10 Bis-Tris Propane (pH=7.4 acetic acid). To determine Ca²⁺ permeability extracellular Na⁺ was lowered to 90 mM and extracellular CaCl₂ was increased to 3 mM and 10 mM, compare to 1 mM Ca²⁺ control. To better resolve calcium permeability, the Na⁺ free solution was used except CaCl₂ was increased ten-fold, 18 mM CaCl2 (in mM): 115 NMDG, 18 CaCl₂, 10 Bis-Tris Propane, (pH 7.4 acetic acid). Osmolarity was measured for each solution and was maintained at 240 mOsm by the addition of sucrose. All recordings were done at room temperature. We used 3M KCl filled electrodes with a resistance between 1-3 MΩ. We used a 3M KCl agar bridge to minimize liquid junction potentials, and all liquid junctions potentials arising at the tip of the recording electrode were corrected online.

Data analysis. Data acquisition and analysis were performed using Axograph (Axon Instruments) software, and curve fitting and statistical analysis were performed with Prism (Graphpad). Dose-response curves from individual oocytes were normalized to the maximum and minimum values and averaged for at least eleven oocytes. Normalized data were fit to the four-parameter equation derived from the Hill equation: Y=Min+(Max−Min)/(1+10(Log EC50-X)(nH)), where Max is the maximal response, Min is the response at the lowest drug concentration, X is the logarithm of agonist concentration, EC50 is the half-maximal response, and nH is the Hill coefficient. Error bars represent the standard error of the mean.

Reversal potential values represent averaged linear regression measurements of individual experiments above and below the point of X-axis intersection. Because the PBO-5/PBO-8 receptor exhibits rectification we used linear regression from −15 to +15, where the relationship is most linear, to determine the reversal potential. Error bars represent the standard error of the mean.

Results

pbo-5 Behavioral Analysis

Recessive alleles in the pbo-5 gene result in a strong posterior body contraction defective (Pbo) phenotype. The posterior body contraction is completely absent from these mutants while the other aspects of defecation such as anterior body contraction, enteric muscle contraction, and cycle timing remain unaffected. Other behaviors including locomotion, egg laying, feeding and mating are also normal.

In contrast to the recessive pbo-5 alleles, two dominant mutations, n2331 and ox7, result in a distinctive hypercontracted phenotype known as posterior body cramp. Specifically, when the defecation cycle is initiated in these mutants, the posterior body muscles contract but fail to immediately relax, and the enteric muscle contraction occurs while the posterior body wall muscles are still contracted. As the animals move, the posterior body muscles eventually relax and the next cycle can be observed.

pbo-5 Cloning

The pbo-5 gene was mapped to the right arm of chromosome V and cloned (FIG. 2). The Y44AE predicted open reading frame encodes pbo-5, confirmed by mutant allele sequencing (Table 1). Furthermore, a mini-gene construct containing the pbo-5 cDNA fused to 4.4 kb of sequences upstream of the second exon rescues the phenotype of pbo-5(ox24) mutants.

TABLE 1 pbo-5 mutations Allele Mutation Protein Exon/Domain ox35 ox36 sa243

Q 59 stop Q 59 stop W 235 stop 2 2 5 N2331dm ox7dm ox38 ox34 sa297 ox9 sa242

L 316 F L 316 F T 304 I P 325 L M 342 T H 184 Q P 181 L 5(M2) 5(M2) 5(M2) 5 (M2-M3 loop) 6 (M3) 4 (LBD) 4 (LBD) ox5 Splice Intron 4 n2330 ox4 ox24 ox26 ox27 ox30 ox32 ox39

pbo-5 Encodes a Ligand-Gated Ion Channel

The primary structure of the pbo-5 cDNA was determined by reverse transcription and polymerase chain reaction. The pbo-5 cDNA includes an SL1 trans-spliced leader sequence at the 5′ end and a total of 9 exons spanning a 7 kb genomic region (FIG. 2). The pbo-5 mutations fall into four categories: (1) nine deletions (2) three nonsense (3) seven missense, and (4) one splice junction mutation (Table 1). The predicted pbo-5 cDNA encodes a 499 amino acid protein (FIG. 3).

BLAST and protein motif queries of PBO-5 suggest that it is a member of the ligand-gated ion channel superfamily. Ligand-gated ion channels are oligomeric receptor complexes containing an integral ion channel that is opened upon ligand binding (Betz, 1990). Ion channels that are gated by acetylcholine, serotonin, γ-aminobutyric acid, and glycine are a superfamily of homologous neurotransmitter receptors, termed the cys-loop superfamily. Although over 100 ligand-gated ion channel subunits have been identified in numerous organisms, each subunit can be assigned to one of the four receptor families based on sequence similarity, and/or functional activity. All ligand-gated ion channel subunits share a common structural and functional homology and have a high degree of amino acid similarity. The subunits are demarcated by a signal peptide, an extracellular amino-terminus that contains consensus ligand binding sites and an invariant disulfide bonded loop (cys-loop), four transmembrane domains (M1-M4), a large cytoplasmic loop between M3-M4, and a short extracellular carboxy terminus (Karlin and Akabas, 1995; Ortells and Lunt, 1995) (FIG. 2). Electron microscopy, electrophysiological and structural data suggest that ligand-gated ion channels are formed from five homologous subunits that are pseudo-symmetrically arranged around a central ion channel, such that the M2 domain lines the ion-channel wall and determines ion selectivity (Betz, 1990; Brejc et al., 2001; Unwin, 1993).

Hydropathy plots and alignment of PBO-5 with various ligand-gated ion channel subunits demonstrates that PBO-5 contains the hallmarks of ligand-gated ion channels (FIG. 3). Additionally, PBO-5 contains many residues that underpin the conserved secondary structure of the cys-loop ligand-gated ion channel superfamily (Brejc et al., 2001). BLAST searches of PBO-5 against human, mouse, Drosophila, and C. elegans genomes suggest that PBO-5 most closely resembles cholinergic receptors. However, phylogenetic analysis demonstrates that PBO-5, and related orthologs, represents a divergent subunit that cannot be categorized into one of the four families based on sequence similarity (FIG. 4). BLAST searches against the C. elegans genome revealed another predicted protein, PBO-8, which contained high sequence identity to PBO-5. For example, accession numbers P12389, O08952 and Q7T2T8. Based on sequence similarity and residues known to be involved with specific ligand sensitivity, the ligand for the PBO-5 receptor was not clearly identifiable from the native sequence. Further, mutants that are defective in GABA, acetylcholine, serotonin, and peptidergic neurotransmission do not exhibit posterior body contraction defects. Therefore, it seemed unlikely that PBO-5 would be activated by known classical neurotransmitters.

pbo-5 is Expressed in the Posterior Body Wall Muscles

If PBO-5 is the receptor that mediates posterior body contraction then it should be expressed in the body wall muscles. To determine the cellular expression of pbo-5, a transcriptional pbo-5::gfp fusion gene was constructed that contained 3.8 kb upstream sequence of the translational start codon fused to the GFP open reading frame (Chalfie et al., 1994). Stable chromosomally integrated lines of this construct expressed GFP in the most posterior muscle cells of the tail and in a small number of neurons in the head (FIG. 5). The expression pattern of PBO-5 demonstrates that it is expressed in the appropriate cells to mediate posterior body contraction.

PBO-5 is not Activated by Classical Neurotransmitters

To determine if PBO-5 can form a homo-oligomeric receptor, we injected PBO-5 cRNA in Xenopus oocytes. Since sequence information did not confidently predict the ligand that would activate the putative PBO-5 receptor, a candidate approach was undertaken to ascertain the ligand. Two-electrode voltage clamp recordings were used to assay receptor functionality. A host of classical neurotransmitters such as acetylcholine, choline, GABA, glycine and serotonin were applied to PBO-5 injected oocytes, yet all ligands failed to elicit a functional response.

Typically, muscle type acetylcholine receptors require both α and non-α subunits to form functional receptors. The predicted PBO-8 protein is the most closely related to PBO-5 of all predicted cholinergic-like receptors in C. elegans (FIG. 4).

PBO-8 Primary Structure and Expression

The pbo-8 predicted open reading frame encodes a protein that is homologous to ligand-gated ion channels (FIG. 3). Significantly, the PBO-8 protein most closely resembles PBO-5 (FIG. 4). To determine the primary structure of PBO-8 RT-PCR was performed and full-length cDNA clones isolated. The PBO-8 full-length cDNA consists of 13 exons that span 4.1 kb of genomic DNA (FIG. 6A). The PBO-8 cDNA encodes a 423 amino acid protein (FIG. 6A). We performed protein alignments with PBO-8 and PBO-5 revealing they share 35% identity. With the exception of one conservative amino acid change, the residues in the M2 domain are identical (FIG. 3). If PBO-8 oligomerizes with PBO-5 to form a functional receptor, then PBO-8 should have overlapping expression with PBO-5. To address the expression pattern of PBO-8, a transcriptional fusion containing 4 kb of upstream promoter sequence fused to GFP was constructed. GFP expression was observed in the most posterior body wall muscles in the tail, identical to PBO-5 expression (FIG. 6B). These data suggest that PBO-8 may oligomerize with PBO-5 to form a functional receptor.

PBO-5/PBO-8 Forms a If-Gated Ion Channel

To determine if PBO-5 and PBO-8 can co-assemble to form a functional receptor, we injected PBO-5 and PBO-8 cRNA into Xenopus oocytes. Agonists which function at other ligand-gated ion channels (such as, ACh, GABA, glycine, 5-HT, glutamate, and choline) lacked the ability to activate PBO-5 homomers, PBO-8 homomers or PBO-5/PBO-8 heteromers. Activation of receptors was not unexpected because genetic evidence demonstrates acetylcholine, GABA, glutamate and serotonin are not required for posterior body contraction. To determine the possible signal that mediates posterior body contraction we examined the pbo-4 gene.

The predicted pbo-4 gene encodes a protein related to Na⁺/H⁺ exchangers. PBO-4 is expressed in the posterior intestine and is required for posterior body contraction. Na⁺/H⁺ exchangers mediate the exchange of one Na⁺ into the cell for one H⁺ out of the cell. The expression of PBO-4 in the posterior intestine parallels the expression pattern of PBO-5 and PBO-8 in the posterior body wall muscles. These data suggest that PBO-4 mediates the secretion of H⁺ from the intestine, into the pseudocoelomic space, adjacent to PBO-5/PBO-8 posterior muscle expression. Therefore, without wishing to be bound by theory, we hypothesized that H⁺ ions may activate or may be required for co-activation of PBO-5/PBO-8 receptors.

To determine if H⁺ ions are sufficient to activate PBO-5/PBO-8 receptors, we applied test pulses of varying pH to PBO-5/PBO-8 expressing cells. Test pulses of pH 6.8 evoked robust inward currents, indicating that H⁺ ions are sufficient to activate recombinant receptors (FIG. 7, inset). To demonstrate that current responses evoked by changes in pH were not due to endogenous channels or transporters, we applied maximal test pulses of pH 5.0 to water injected and uninjected oocytes. Only oocytes injected with PBO-5/PBO-8 cRNA exhibited H⁺-gated responses. To determine if PBO-5 and PBO-8 can form functional homomeric H⁺-gated ion channels, we injected each subunit alone into oocytes. Injection of PBO-5 or PBO-8 cRNA into oocytes, resulted in little or no functional expression compared to oocytes co-injected with PBO-5 and PBO-8 cRNA. These data suggest that the PBO-5/PBO-8 heteromultimerization is required for efficient functional receptor expression in vitro.

H⁺ ions have been demonstrated to modulate classical synaptic transmission. For example, acidic changes in pH inhibit acetylcholine receptor function, where alkaline environments enhance receptor function (Palma et al., 1991; Pasternack et al., 1992). To determine whether or not classical neurotransmitters co-activate PBO-5/PBO-8 receptors, we applied pH 6.8 with and without 1 mM ligand. Application of pH 6.8 plus acetylcholine, choline or GABA was not significantly different from pH 6.8 only application (data not shown). Taken together, these data suggest that H⁺ ions alone are sufficient to fully activate PBO-5/PBO-8 receptors.

To determine the pH50 (half-maximal activation) of PBO-5/PBO-8 heteromultimers, we first identified the pH range at which the recombinant receptors were activated. We determined that the PHIO (10% maximal activation) was approximately pH 7.0. We set our perfusion buffer at pH 7.4 for all experiments, where no activation of recombinant receptors was observed. A pH₅₀=6.83±0.01 was determined by applying decreasing pH test pulses (pH 7.0-5.0). A steep Hill coefficient of 9±0.66 was determined, demonstrating PBO-5/PBO-8 receptors exhibit significant H⁺ binding cooperativity (FIG. 7).

PBO-5/PBO-8 Ion-Selectivity

Current-voltage (I-V) analysis was used to characterize the ionic conductance underlying PBO-5/PBO-8 responses. The H-gated current had a reversal potential of 10.18±0.80 mV in Ringer's solution (FIG. 8A). The I-V relationship demonstrates that PBO-5/PBO-8 exhibits inward rectification (FIG. 8A, inset). The positive reversal potential suggests that PBO-5/PBO-8 encodes a cation-selective ion channel. To determine if Na⁺ underlies PBO-5/PBO-8 H⁺-evoked responses, we replaced Na⁺ with the large cation N-methyl D-glucamine In Na⁺-free solution, the inward current was eliminated and the reversal potential was −82.90±8.13 mV (FIG. 8B). Furthermore, to demonstrate anions such as Cl⁻ do not flow through PBO-5/PBO-8 channels, we replaced extracellular Cl⁻ with the impermeable anion gluconate. In C⁻ free solution, the inward current remained with no significant shift in reversal potential (ΔE_(rev)=0.25 mV, P>0.05, two-way ANOVA), compared to control (FIG. 8C). This demonstrates Na⁺ is the primary charge carrier through PBO-5/PBO-8 channels.

To determine the cation-selectivity of the PBO-5/PBO-8 ion channel, we substituted extracellular Na⁺ with equivalent K⁺. In K⁺ Ringer's solution, I-V relationships were not significantly different (P>0.05 two-way ANOVA) compared to Na⁺ Ringers control (FIG. 8D). Additionally, strong inward rectification was present in I-Vs determined in K⁺ Ringers, demonstrating rectification was not due to ion-selectivity. Taken together, these data demonstrate PBO-5/PBO-8 encodes a non-selective inwardly rectifying cation channel.

Next, Ca²⁺ permeability of the PBO-5/PBO-8 ion channels was assayed. The 1-V relationships under three Ca²⁺ concentrations: 1 mm control, 3 mM, and 10 mM, were determined Increasing calcium to 10 mM resulted in a positive shift in reversal potential from control (FIG. 9A). To better resolve calcium permeability, NaCl was replaced with NMDG in the extracellular solution, making Ca²⁺ the only relevant extracellular ion. Increasing Ca²⁺ in this solution revealed that PBO-5/PBO-8 channels are calcium permeable. Increasing Ca²⁺ 10 fold caused a +50 mV shift in reversal potential compared to control (FIG. 9B).

Interestingly, H⁺-evoked inward currents were significantly reduced as extracellular Ca²⁺ was increased (FIG. 9). Specifically, a control pulse of pH 6.8 with 1.0 mM Ca²⁺ evoked a large response, and an equivalent test pulse of pH 6.8 with 10.0 mM Ca²⁺ evoked a much smaller response. This suggests that, while Ca²⁺ is permeable, high amounts of Ca²⁺ inhibit gating of PBO-5/PBO-8 channels.

To further investigate the Ca²⁺ inhibition of PBO-5/PBO-8 receptors, dose response experiments were performed under different extracellular Ca²⁺ conditions (0.1, 1, 3, 10 mM). PBO-5/PBO-8 receptors under 1 mM Ca²⁺ control conditions exhibited a pH₅₀=6.88 and a Hill coefficient of 6 (FIG. 10A). As Ca²⁺ was increased to 10 mM a right shift in the activation curve of PBO-5/PBO-8 was observed. Specifically, a significantly different pH₅₀=6.59 and a Hill coefficient of 4 was determined under 10 mM Ca²⁺ test conditions (FIG. 10A). These data demonstrate that as extracellular Ca²⁺ is increased, H⁺ sensitivity and cooperativity decrease.

Next, to determine if increasing extracellular Ca²⁺ caused an inhibition of maximal PBO-5/PBO-8 activation, Ca²⁺ conditions at three different pH ranges (7.0, 6.8, and 6.0) were applied. H-evoked responses were significantly reduced, compared to 1 mM Ca²⁺ control, at pH 7.0 and 6.8 as Ca²⁺ was increased to 3 mM and 10 mM (FIG. 10B). However, at pH 6.0, increasing extracellular Ca²⁺ had no effect on maximal activation of PBO-5/PBO-8 (FIG. 10B). These data suggest that Ca²⁺ acts as a competitive antagonist at PBO-5/PBO-8 receptors. We are further examining the mechanism of Ca²⁺ antagonism to PBO-5/PBO-8 receptors.

Discussion

It is demonstrated that pbo-5 encodes a novel ligand-gated ion channel subunit required to initiate the posterior body contraction of the defecation cycle. Loss of pbo-5 activity specifically eliminates the posterior body contraction, while gain-of function alleles result in hypercontraction of the posterior body muscles. PBO-5 is expressed in the most posterior muscle cells of the tail, suggesting it is properly localized to mediate the posterior body contraction. Finally, it is demonstrated that PBO-5 heteromultimerizes with PBO-8 to form a novel H⁺-gated ion channel when expressed in Xenopus oocytes. The channel encoded by PBO-5/PBO-8 is a nonselective inward rectifying cation channel. The molecular identification and functional characterization of the PBO-5 and PBO-8 receptor subunits defines a novel group of the cys-loop ligand-gated ion channel superfamily. Furthermore, the functional characterization of H⁺-sensitivity demonstrates that the PBO-5/PBO-8 signaling pathway defines a novel mechanism of cellular communication.

H⁺ Dependence of PBO-5/PBO-8

The overlapping cellular expression of PBO-5 and PBO-8 in the most posterior body muscles of that tail, coupled with the fact that functional receptor expression is only observed when both PBO-5 and PBO-8 are coinjected into oocytes, strongly suggests the PBO-5/PBO-8 represents the native receptor that mediates posterior body contraction. We have demonstrated that H⁺ ions are sufficient to activate PBO-5/PBO-8 receptors.

The defecation cycle in a wild-type animal occurs every 50 seconds with little variability and the first muscle contraction to occur is the posterior body contraction. It has been demonstrated that periodic calcium release in the intestine correlates with the onset of the posterior body contraction (Dal Santo et al., 1999). The itr-1 gene which encodes an inositol triphosphate (IP₃) receptor is required in the intestine for proper defecation cycle timing (Dal Santo et al., 1999). Hypomorphic itr-1 alleles exhibit long or no defecation cycle cycles (>50 seconds), while overexpression of itr-1 results in short defecation cycle times (<50 seconds). Furthermore, calcium imaging of itr-1 hypomorphic alleles that have no defecation cycles (i.e., no posterior body contraction) fail to exhibit calcium oscillations (Dal Santo et al., 1999). Taken together, these data suggest that IP₃ receptor activity in the intestine is required for the signaling of each muscle contraction in the defecation cycle.

The posterior body contraction is the initial contraction in the defecation motor program, and does not rely on neuronal input. The PBO-5/PBO-8 receptor is gated by H⁺ ions, and PBO-5 is required for posterior body contraction. It has been demonstrated that IP₃ receptor (itr-1) mediated calcium signaling in the intestine is required for the activation of the posterior body contraction (Dal Santo et al., 1999). However, the nature of the signal was unknown as mutants with defects in classical neurotransmission have normal posterior body contraction.

The pbo-4 gene encodes a protein that has similarity to Na⁺/H⁺ exchangers (NHEs). pbo-4 mutants are phenotypically identical to pbo-5 mutants, and the pbo-4; pbo-5 double mutant is identical to both single mutants. This suggests that pbo-4 and pbo-5 are in the same signaling pathway that mediates posterior body contraction.

Furthermore, the expression pattern of pbo-4 is restricted to the posterior intestine, adjacent to the muscle expression of PBO-5 and PBO-8. Na⁺/H⁺ exchangers have been implicated in a number of processes including intracellular pH and cell volume regulation, and in reabsorption of NaCl across epithelial cells (Counillon and Pouyssegur, 2000; Orlowski and Grinstein, 1997). Plasma membrane NHEs mediate the electroneutral exchange of Na⁺ ions into the cell for H⁺ ions out, thereby acidifying the extracellular environment while increasing intracellular pH. Mammalian NHEs are regulated by a number of factors including phosphorylation, calcium, and by interactions with accessory proteins (Orlowski and Grinstein, 1997). For example, mammalian NHE1 is sensitive to increases in cytosolic Ca²⁺, due to a high-affinity calmodulin binding site present on the C-terminal tail of the protein (Bertrand et al., 1994). Deletion of this binding site causes NHE1 to be constitutively active (Wakabayashi et al., 1994; Wakabayashi et al., 1997). Therefore, under normal conditions (low Ca²⁺), the calmodulin-binding site is unoccupied and exerts an inhibitory effect. An intracellular rise in Ca²⁺ stimulates Ca²⁺/calmodulin binding to NHE1, thereby releasing inhibition, and activating Na⁺/H⁺ exchange. Analysis of the C-terminal tail of the PBO-4 protein predicts a putative calmodulin binding site as well as a consensus phosphorylation site for CaMKII.

The structural analysis and expression of pbo-4 in the intestine predicts that PBO-4 mediates the exchange of Na⁺ ions into the intestine for H⁺ ions out of the intestine into the pseudocoelomic space. H⁺ binding has been demonstrated herein to be sufficient to activate PBO-5/PBO-8 receptors. Therefore, without wishing to be bound by theory, it is believed that the H⁺ signal arises from the intestine and H⁺ transport is mediated by PBO-4.

It has been demonstrated that IP₃ receptor mediated release of calcium from the intestine correlates with the onset of the posterior body contraction and is required. Therefore, it is believed that a necessary feature of the posterior body contraction signaling mechanism is that it be modulated by calcium. The pbo-4 gene, expressed in the posterior intestine, encodes a Na⁺/H⁺ exchanger with a predicted Ca²⁺/calmodulin binding domain. It has now been demonstrated that H⁺ ions are sufficient to activate PBO-5/PBO-8 receptors (e.g., using Xenopus oocytes (in vitro)) that are localized to the posterior body muscles.

Without wishing to be bound by theory, from this data it is proposed that for posterior body contraction: 1) IP₃ receptors localized to the smooth endoplasmic reticulum in the intestine are activated every 50 seconds. Activation results in the intracellular rise of Ca²⁺ in the intestine; 2) Ca²⁺ binds to the C-terminal calmodulin-binding domain of PBO-4, thereby activating H⁺ transport activity; 3) PBO-4 transports H⁺ ions out of the intestine acidifying the pseudocoelomic space; and 4) H⁺ ions bind and activate the PBO-5/PBO-8 receptors expressed in posterior body wall muscle, thereby allowing Na⁺ influx into the cell causing a depolarization and subsequent muscle contraction (FIG. 11).

This simple model can account for the non-neuronal nature of the posterior body contraction, and involves strict calcium regulation. The present invention demonstrates that PBO-5/PBO-8 receptors are exquisitely sensitive to changes in extracellular pH, as determined in heterologous cells (pH₅₀=6.83±0.01). The sensitivity of PBO-5/PBO-8 receptors suggests minor acidification of the pseudocoelomic space is required to activate the posterior body contraction. The pseudocoelomic space separates the intestine from the muscle, and is relatively small as observed in electron micrographs. Thus, the acidification of the pseudocoelomic space at the posterior end of the animal to a pH ˜6.8 is not physiologically unreasonable. In vivo recording from the posterior body wall muscles is preformed to recapitulate the in vitro findings.

PBO-5/PBO-8 is a Novel Cys-Loop Ligand-Gated Ion Channel

The PBO-5 and PBO-8 subunits display the structural motifs common to the superfamily of cys-loop ligand-gated ion channels. However, the distinctive sequence and functional activity prevent classification within any of the four established receptor families. Motor behaviors, such as muscle contraction, are typically controlled via fast synaptic transmission between a motor neuron and muscle cell. The present invention demonstrates that H⁺ ions alone are sufficient to activate recombinant receptors and that co-application of other classical neurotransmitters has little effect on activation. Furthermore, the functional characterization of the receptor and proposed model of excitation provide a unique form of fast non-synaptic communication. Protons have been demonstrated to be modulatory at “cys-loop” ligand-gated ion channels; however, this is the first evidence that protons can directly activate this receptor subclass. Therefore, the present invention demonstrates that H⁺ fulfills the criteria of a fast transmitter in C. elegans.

In one exemplary embodiment mammalian paralogs and/or orthologs are identified, for example by BLAST searches using PBO-5 and PBO-8 sequences (e.g. SEQ ID NOS: 6 and 7), and one or more of the paralogs and/or orthologs is confirmed to be a component of a H⁺-gated ion channel. In particular, there are a number of predicted cholinergic-like proteins to which PBO-5 and PBO-8 share identity. Changes in extracellular pH have been demonstrated to regulate ion channel function, hi most cases, H⁺ ions modulate classical neurotransmission by inhibiting or exciting various classical ligand-gated ion channels. While it has been demonstrated that H⁺ signaling is a major pathway for pain sensation through the acid-sensing ion channels (ASIC), direct H⁺ signaling has never been associated with cys-loop ligand-gated ion channels (Waldmann et al., 1997; Waldmann et al., 1999).

Recently, a novel Zn²⁺ activated ligand-gated ion channel (ZAC) has been cloned and characterized in humans (Davies et al., 2003). The ZAC channel represents a distinct class of cys-loop ligand-gated ion channels that is not activated by classical neurotransmitters. Interestingly, the ZAC subunit has been retained in some mammals (human and dog), but has been lost by others (mouse and rat), demonstrating specific cell signaling mechanisms may vary across species. Therefore, an exemplary embodiment of the invention provides a method for the identification and characterization of the H⁺ gated PBO-5/PBO-8 receptor in other species.

In an exemplary embodiment, the pharmacology of the PBO-5/PBO-8 receptor is determined, in another exemplary embodiment modulation of PBO-4 by Ca²⁺ is determined In yet another exemplary embodiment, isolation of PBO-8 mutants is performed and the mutant phenotype assayed relative to PBO-5 and/or PBO-4. Optionally, genetic analysis is conducted to determine if PBO-8 is in the same genetic pathway as PBO-5 and/or PBO-4.

To determine if H⁺ ions are required to initiate a posterior body contraction endogenous acidification of the pseudocoelomic space is blocked. For example, 100 mM Bis-Tris Propane buffered saline (pH 7.2) is injected into the pseudocoelomic space of an animal and defecation cycles postinjection observed. It is believed that animals that have had buffered saline injected into the pseudocoelomic space will fail to initiate a posterior body contraction while all other steps of the defecation cycle will be normal. The injected animals should phenocopy both pbo-4 and pbo-5 mutants.

Alternatively, a caged buffer is used to assay the requirement for H⁺ activation of PBO-5/PBO-8 receptors in vivo. For example, animals are injected with a caged buffer (Molecular Probes) and the buffer uncaged, by flash photolysis, as a posterior body contraction is about to occur. An advantage of the latter scheme is that an animal can be injected first and then observed for a number of cycles to determine if it retains normal defecation cycles, and in particular posterior body contractions. After quantification of a number of defecation cycles, the buffer is uncaged and the animal observed for a specific loss of posterior body contraction. Li addition, the inverse experiment, where caged protons are injected, may be conducted to elicit an out of phase posterior body contraction by uncaging the protons during the intercycle.

Functional Analysis of Dominant pbo-5 Alleles

Several of the pbo-5 mutations provide particularly interesting insights into the structure and function of the PBO-5 protein. Loss-of-function mutations cause an absence of posterior body contraction, while gain-of-function mutations cause hypercontraction. Two dominant alleles (n2331 and ox7) result in the same mutation within the M2 domain of the ion channel. Specifically, residue 316 is mutated from leucine to phenylalanine (L316F). The M2 domain lines the ion channel wall, and residues in and around M2 affect ion selectivity and receptor desensitization (Leonard et al., 1988). An adjacent residue is altered in the M2 domain of the cholinergic DEG-3 gain-of-function mutant, and causes cell death (Treinin and Chalfie, 1995). It was proposed that prolonged opening and increased ion flow through DEG-3 ion channels underlies the degeneration. Similarly, dominant gain-of-function mutations within the M2 domain of acetylcholine receptors leads to increased ion flow through slower channel closure (Engel et al., 1996). Therefore, it is believed that the cramp phenotype observed in the dominant alleles is due to a channel that has slower inactivation.

To determine if pbo-5 (n2331dm) encodes a slowly inactivating receptor, cDNAs that carry the mutation are isolated and pbo-5 (n2331dm) cRNA is coexpressed with wild-20 type PBO-8, and receptor function is assayed. It is believed that pbo-5 (n2331dm) will result in a response to acidic pH application that is prolonged and enduring, rather than desensitizing as in the wild-type.

PBO-5/PBO-8 Pharmacology

PBO-5/PBO-8 forms a heteromultimeric H⁺-gated cation channel and extracellular Ca²⁺ concentration affects PBO-5/PBO-8 pH sensitivity. The PBO-5/PBO-8 receptor subunits are structurally related to the ligand-gated ion channel superfamily, and sequence analysis and functional activity place the PBO-5/PBO-8 receptor into a previously unknown family (FIG. 4). hi an exemplary embodiment, H⁺-gated cation channel receptors are identified and assayed for sensitivity to known ligand-gated ion channel agonists and antagonist. In addition, H⁺-gated cation channel receptors are identified in a subject, for example, a mammalian or vertebrate subject, such as a human, and assayed for functions described herein. Such mammalian, or vertebrate, receptors are assayed for drug interactions with have agonist, antagonist or blocking activity.

For example, it was observed during electrophysiological investigation of PBO-5/PBO-8 that the buffer HEPES (N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid) in our extracellular solution produced a very rapid rundown of the H⁺-evoked current that could not be explained by poor oocyte health. An initial pulse of pH 6.8 HEPES buffered solution gave a robust inward current. However, subsequent application of pH 6.8 HEPES caused a marked reduction in inward current. Eventually, PBO-/PBO-8 receptors could be run-down to zero current with repeated pH 6.8 applications that was not reversible with time or supramaximal pH 5.0 application. Initially an extracellular ion replacement was conducted, since a divalent ion such as Ca²⁺ could impart the current block. However, Ca²⁺ reduced solutions still exhibited use-dependent block, therefore, the buffer containing HEPES was substituted with Bis-Tris Propane (1,3-Bis[tris(hydroxymethyl)methylamino) propane or MES (2-(N-Morpholino)-ethanesulfonic acid.

When HEPES was replaced with either Bis-Tris Propane or MES, repeated acidic pH test pulses did not cause current run-down. Therefore, HEPES was shown to be inhibitory to the receptor. Furthermore, HEPES was demonstrated to be the relevant blocking molecule by applying pH 6.8 pulses of HEPES buffered solution until the evoked current was run down to zero. Following pulsed run down, a pH 6.8 pulse of Bis-Tris propane was applied to the run down receptors. Application of pH 6.8 Bis-Tris Propane or MES buffered solutions to rundown receptors, evoked a robust inward current. Specifically, a current equal to or greater than the initial pH 6.8 HEPES response was obtained.

How can HEPES be inhibiting the channel? Recently, the structure of an acetylcholine binding protein (AChBP) that is homologous to the N-terminus of acetylcholine receptors has been resolved (Brejc et al, 2001). The structure of this protein agrees with the predicted N-terminal structure of ligand-gated ion channels. Importantly, it was determined that the ligand binding sites are located at each of the five subunit interfaces, which are located in the extracellular N-terminal part of the protein. Interestingly, the resolved crystal structure contained a HEPES molecule present in each ligand-binding site. In the structure it was determined that HEPES made no specific hydrogen bond with the protein, but its quaternary ammonium group stacked onto Trp143 making cation-π interactions (Brejc et al., 2001). These data suggest that the HEPES molecule may be occluding the H⁺-binding site of PBO-5/PBO-8 receptors. In an exemplary embodiment, mutations are made in and around the presumptive ligand-binding pocket and assayed for abolishment of HEPES inhibition.

As the PBO-5/8 receptor is exclusively activated by H⁺, it was next determined if PBO-5/8 gating could be blocked with amiloride. Amiloride is a commonly used pharmacological agent used to block acid sensing ion channels (ASIC). Application of 1 mm amiloride to PBO-5/8 expressing cells did not result current block, demonstrating the H-gating mechanism of PBO-5/8 receptors is different from the ASIC channels. Furthermore, common cholinergic antagonist such as d-tubocurare were applied to PBO-5/8 expressing cells, but all attempts to pharmacologically block PBO-5/8 responses failed. These data suggest the gating mechanism of PBO-5/8 receptors is quite different from both cholinergic and ASIC receptors.

In an exemplary embodiment, other compounds which bind the ligand binding pocket, for example, of a vertebrate H⁺-gated channel, which may be identified by the methods of the present invention, are assayed. In one exemplary embodiment, agonists and/or antagonists are identified. In another exemplary embodiment, an agonist and/or antagonist is manufactured as a medicament for the treatment of conditions relating to activation or inactivation of the H⁺-gated channel.

PBO-4 Characterization

It has been demonstrated that initiation of the defecation cycle is a highly calcium regulated process, and that calcium spikes in the intestine correlate with the onset of the posterior body contraction (Dal Santo et al., 1999). Therefore, it is believed that the defecation cycle regulated by calcium. The pbo-4 gene encodes a putative Na⁺/H⁺ exchanger that is expressed in the posterior intestine. Without wishing to be bound by theory, it is believed that calcium release in the intestine, through IP₃ receptors, results in the activation of PBO-4. Specifically, PBO-4 contains a consensus calmodulin-binding domain that is thought to be inhibitory to transport activity. Therefore, to activate PBO-4, Ca²⁺ would bind the calmodulin site, thereby releasing inhibition and allowing proton transport, hi an exemplary embodiment, the secretion of H⁺ by PBO-4 from the intestine, in a calcium dependent manner, PBO-4 is assayed for calcium binding and proton transport activity.

The posterior body contraction occurs via a calcium-regulated mechanism. The cloned and characterized pbo-4 gene, which encodes a Na⁺/H⁺ exchanger, is expressed on the basolateral surface of the posterior intestinal cells, juxtaposed to the posterior body wall muscles. Utilizing caged protons, it has been demonstrated that acidification of the pseudocoelomic space, which separates the intestine from the body wall muscles, was sufficient to activate the posterior body contraction in vivo. These results suggest that PBO-4 Na⁺/H⁺ transport activity is required to activate the posterior body contraction. Importantly, the identification of the PBO-5/8 receptor confirms that H⁺ ions function as a primary transmitter in C. elegans. Furthermore, these results demonstrate that Na⁺/H⁺ exchangers can function as a regulated H⁺ release mechanism that mediates cellular signaling.

pbo-4 Mutations:

Allele Nucleotide Change Protein Change Sa300 GGA → AGA G318R n2658 GGTATTAA(Δ548 bp) GACAC Deletion of the C-terminus ok583 GCGACTCA (Δ1.702 Kb) aatttt Deletion of TM3-TM12 ok10 GCA → GAA A717D . . . 5 aa . . . Stop PBO-8 Behavioral Characterization

In another exemplary embodiment, a deletion library is screened to identify an allele, for example, an allele of pbo-8. Optionally, RNAi technology may be used to knock out expression of PBO-8 or an ortholog/paralog identified in another organism. Any assay known in the art may be used to study a PBO-4, PBO-5, and/or PBO-8 ortholog/paralog, for example, RNAi technology, see U.S. Patent Applications 20030153519, 20030175772, 60/528,567, 60/518,856.

While this invention has been described in certain embodiments, the present invention can be further modified within the spirit and scope of this disclosure. This application is therefore intended to cover any variations, uses, or adaptations of the invention using its general principles. Further, this application is intended to cover such departures from the present disclosure as come within known or customary practice in the art to which this invention pertains and which fall within the limits of the appended claims.

All references, including sequence accession numbers, publications, patents, and patent applications, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.

REFERENCES

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1. A method of screening a candidate compound, the method comprising: (a) introducing a nucleic acid sequence that encodes an amino acid sequence having 80% identity to PBO-4 (SEQ ID NO:8) into a host cell; (b) expressing the nucleic acid sequence to produce a H⁺/Na⁺ exchanger in the host cell; (c) contacting the host cell with a candidate compound; and (d) screening for activation or inhibition of the H⁺/Na⁺ exchanger by the candidate compound.
 2. The method of claim 1, further comprising: (a) introducing a nucleic acid sequence encoding PBO-5 (SEQ ID NO:2 or SEQ ID NO:6) into a host cell; and (b) expressing the nucleic acid sequence to produce a H⁺/Na⁺ exchanger in the host cell.
 3. The method of claim 1, further comprising: (a) introducing a nucleic acid sequence encoding PBO-8 (SEQ ID NO:3 or SEQ ID NO:4 or SEQ ID NO:7) into a host cell; and (b) expressing the nucleic acid sequence to produce a H⁺/Na⁺ exchanger in the host cell.
 4. The method of claim 1, further comprising producing the candidate compound.
 5. The method of claim 1, further comprising identifying a compound that prevents binding of HEPES to the ligand-gated cation channel. 